Back in the day I saw this bug (although it was the other category taking up all the space) - on a retail unit in the Apple store I was working at. The other section was taking up too much space on the 3GS 8GB demo unit, causing the restore from backup at night to fail.
I brought it to the attention fo Retail Engineering via email and he thought I was nuts but forwarded it to software QA anyway. 24 Hours later I hear back that they found a corruption issue in the software. I wasn't nuts. They fixed it in the next update.
A variant of this issue seems to happen to people randomly on a variety of iOS devices (even the series 3 watch upgrade last week.)
I'm surprised after 14 versions of iOS that apple hasn't fixed the storage system to eliminate these fake full storage scenarios, but I lack the software engineering knowledge to comprehend why it happens or how to fix outside of reboots and restores.